KAZO, Uganda — In this remote village near Uganda’s Rwenzori Mountains, the landscape of the African savannah stretches out over rolling hills with tawny grass, green clusters of bushes, and short trees. Occasionally, white smoke rises from a field where a farmer is burning brush.

This is malaria country.

More than half of the children under 5 in Kazo have the malaria parasite present in their blood, according to a survey by the aid group Doctors Without Borders. Fifty-nine percent of the Kazo health center’s outpatient visits by children, and fully two-thirds of the visits by the rest of its outpatients, were spurred by the omnipresent mosquito-borne disease. Across the country, anywhere from 19,000 to more than 70,000 children under 5 die of malaria each year, depending on whose statistics are used.

It is here in the rural villages, far from the sprawling capital of Kampala, that the majority of Ugandans live. And it is here that treating malaria is a frontline battle for the country’s health care community to save young lives. But Uganda’s significant progress in reducing child mortality and malaria may be threatened by a growing disparity between health centers funded by Uganda’s corruption-wracked government and those operated by nongovernmental organizations, or NGOs.

Kazo health center is a study in the contrasts between Uganda’s overstretched government system and the relative prosperity of the NGOs. Outside the crowded public children’s ward, mothers wait for hours for their children to get medical attention. Directly next door, a special ward has been set up for a study comparing various medication regimes for pediatric malaria. Funded by the University of Antwerp, the study pays for the medicines of children who qualify for participation — medicines that often run out on the public side of the clinic.

Rehema Katusime knows this contrast as well as anyone. She was breastfeeding her 1-year-old daughter, Amina, in a bed in the university’s study ward. Three days earlier, on a Tuesday, Katusime had brought Amina to the clinic because she was vomiting, feverish, and had an unusual dark yellow color to her urine. Amina tested positive for malaria and qualified for the study, which provided her with the antimalarial drug Coartem. By Friday afternoon, Amina’s temperature had receded and she was keeping down her food. Katusime expressed her happiness at Amina’s recovery.

But six months earlier, when her 4-year-old son, Mudasiru, got malaria, Katusime had a very different experience. She brought Mudasiru in on a Friday, already so ill that he was suffering convulsions. Sitting in her bed, Katusime pantomimed her son’s symptoms, twitching her arms up and down spasmodically.

When Mudasiru arrived, the government-funded ward was out of Coartem, and the study ward was not accepting patients. The doctor could only refer the boy to a private clinic, where Katusime and her husband, peasant farmers who grow sweet potatoes and cassava, would have to pay for his medicine. To cover the $200 cost of her son’s treatment, Katusime would have to borrow money from a collective in her village. She had to bring the gravely ill Mudasiru back to her home for the weekend while she raised the necessary money and waited for the private clinic to reopen.

It was not until Monday that she brought Mudasiru to the private clinic, which provided him with medicine before it was too late. Although the boy has recovered, severe malaria cases can often do lasting damage to a child’s cognitive and neurological development. Katusime now lives in fear that one of her children will contract malaria again, and that she will be unable to pay for the treatment.

The director of the Kazo health center, Dr. Franco Zirabamuzaale, said he receives regular shipments of Coartem from the government but consistently runs out of stock in the periods between shipments. During that time, he is forced to refer malaria patients to private clinics.

“You refer and some go back to the village and die there,” said his deputy, senior clinical officer Fausta Nakausi. “You see mothers crying.”

When the health center is out of stock, parents become increasingly desperate for their children to qualify for the University of Antwerp’s study. Rebecca Kabugo, the study’s head nurse, said that parents know that the study screens for new patients on Mondays, and that they sometimes line up outside the clinic on Sunday nights to try to get their children screened the following morning.

When the University of Antwerp completes its study and leaves, the village will be left with the government health center and the nearby private clinics.

“I really don’t like imagining what will happen,” Kabugo said.

A CLIMATE OF CORRUPTION

The problems in Uganda’s health care system and the shortages of the antimalarial drug grow out of the country’s corruption-wracked government. The list of corruption scandals in malaria and child health programs alone is formidable.

In 2005, the Global Fund to Fight AIDS, Tuberculosis, and Malaria suspended more than $200 million in health grants to Uganda due to concerns about misappropriation. In 2007, former health minister Jim Muhwezi and two of his deputies were arrested for theft of child health funds but were acquitted nearly five years later when the case against them was dropped. Last year, three more health officials were arrested for allegedly misusing a $51 million Global Fund grant for malaria. An anticorruption task force has brought more than 83 cases alleging misappropriation of drugs.

In fact, the two most senior health officials to whom government workers referred me for this story — Dr. Myers Lugemwa of the Malaria Control Programme and Ministry of Health Permanent Secretary Asuman Lukwago —have both been charged with embezzlement.

The stream of Ugandan officials facing similar charges of corruption and graft has prompted most European countries to withdraw their support to Uganda’s government for the 2013-14 fiscal year. The cutbacks of more than $280 million represent roughly 90 percent of direct foreign aid to Uganda, with foreign aid constituting about a quarter of Uganda’s budget the previous year. The health sector is particularly reliant of foreign contributions, and while the numbers are difficult to pinpoint, most officials said international aid accounts for the majority of health spending.

This is far from the first time that aid has been suspended, but the swiftness and thoroughness of the withdrawal suggest a possible shift in the politics of foreign aid. Some European donors are now directing donations away from the government and toward NGOs and other third parties. The NGO approach to aid is one that the United States has practiced in corruption-prone countries such as Uganda, even as European nations often advocated direct budget support to allow greater local ownership.

“What’s new and important is the kind of action that was taken,” said Terra Lawson-Remer, a fellow at the Council on Foreign Relations and an expert on development aid. “This might indicate the beginning of a shift toward having less budget support and more support for NGOs.”

It is a shift that Ugandan officials are trying desperately to avoid. Uganda has repaid the stolen money to foreign donors, jailed the embezzlement scheme’s architects, and is urging international contributors to help put in place a system of controls that will reassure them.

So who are the officials who have been accused of corruption inside this struggle to save young lives?

Behind the laboratory where his research team is breeding mosquitoes, Dr. Myers Lugemwa, the deputy director of Uganda’s Malaria Control Programme, has stepped out into the afternoon sun and is vehemently defending his good name.

A middle-aged man with oval-shaped glasses and a perpetually serious expression, Lugemwa has an air of intense conviction that he brings to whatever he does. He brims with information on topics from mosquito behavior to insecticidal sprays, and he insists that given the proper resources he could stamp out malaria in Uganda entirely. When I called him earlier in the afternoon and asked about the corruption charges against him, he urged me to meet him immediately to see the work he was doing for his country and put any such notion to rest. His expression now darkens when he recalls his recent trial.

“I really don’t like to be reminded, because I was in prison there,” Lugemwa said, pointing toward a building not too far away. “It makes me feel like crying.”

In 2010, following a nine-month investigation by an anticorruption unit, Lugemwa and two other leaders of the Malaria Control Programme were charged with illegally selling government malaria drugs to benefit themselves and their families. They were briefly held in jail before facing trial before Uganda’s Anti-Corruption Court. All three were acquitted on the grounds that there was insufficient evidence against them. Impunity for high-ranking officials is pervasive in Uganda, but according to Lugemwa and news reports, there were parts of the government’s case that did not add up. For example, Lugemwa and his colleagues were accused of misappropriating more doses of drugs than the donor in question had provided.

Lugemwa has since returned to his post.

It is hard to miss the personal resonance of Lugemwa’s appeal for donors to return. In addition to fighting his past, he is helping to manage a national malaria program whose insecticide-treated bed nets, antimalarial drugs, and local outreach programs are largely funded by foreign aid. Lugemwa acknowledges that corruption is a problem in Uganda, but he is adamant that he is innocent of the accusations that landed him in court. When I asked him why he thought the government had accused him, he said that the prosecutors were incompetent, and that he was a “sacrificial lamb.”

“What happens in the Bible is what happens on Earth,” Lugemwa said. “They accuse an innocent man and let the thief go.”

Lugemwa said that to maintain progress in the fight against malaria, donors should sit down at the table with Uganda’s government. Uganda has made strong progress in reducing malaria and child mortality in the last decade, with malaria positivity rates for children under 5 dropping by 30 percent and mortality rates dropping by 37 percent.

Pressed further on what might have prompted the charges, Lugemwa said: “I will tell you one thing. Malaria is a political disease.”

BEHIND THE EMBASSY WALLS

To fully understand the politics of malaria aid, it is necessary to take a short journey outside downtown Kampala, the site of Lugemwa’s laboratory and Uganda’s central government. Kampala is a sprawling city of about 2 million people, with roads to its major landmarks radiating outward like spokes of a wheel from the old British colonial headquarters. Where the British once ruled, there now stands an enormous, gorgeously constructed mosque, built as a gift from the late Libyan strongman Moammar Gaddafi.

The quickest method of transportation in Kampala is hopping on the back of ubiquitous motorcycle taxis called boda-bodas. Driven by young men with surprising aggression and precision, the bodas bob and weave through Kampala’s gridlock like water flowing through sand. So I embarked on a boda journey from downtown Kampala to the suburb of Nsambya, where the United States Embassy stands in a massive walled compound and a labyrinth of security checks.

The precautions are understandable: At the time US embassies in North Africa and the Middle East had been shut down because of terrorist chatter. But between the massive walls and onionlike layers of security, one suspects that if the post-Benghazi US State Department guarded its aid money the way it guarded its premises, very few aid dollars would be lost.

One of the men in charge of protecting that aid money is Zdenek Suda, USAID’s supervisory program officer and its acting mission director at the time of my visit. With a salt-and-pepper moustache and blunt manner of speech, Suda said that the problem in Uganda is not the design of its programs but endemic corruption in President Yoweri Musevini’s regime. Working with third parties brings overhead costs of up to 30 or 40 percent, which Suda said was a price USAID paid to avoid the risks of handing money directly to the government.

“There have been a series of major scandals involving the outright theft of tens of millions of dollars,” Suda said. “Very high level, and it’s usually only some lower level schmuck who goes to jail.”

Suda said that last year’s revelations of theft in the office of the prime minister marked a change in the attitudes of European donors. Previously, Suda said, Europeans had promoted a policy of direct budget support that they felt better reflected the spirit of the Paris Declaration on Aid Effectiveness. The declaration was a 2005 agreement among more than 100 developed and developing countries, including the United States, that emphasized national control of development plans.

“Not only do they feel like they got ripped off, they feel like they were embarrassed,” Suda said of European donors in Uganda. “These are the same, the usual suspects — the Irish and the Scandinavians — who were beating the drum about the need to get with the Paris Declaration principles, and country ownership, and let the government take the lead, and it kind of blew up in their face.”

Irish Aid confirmed that it will contribute only to third-party recipients until significant reforms are enacted. The British agency UK AID said that it had also withdrawn direct budget support and would soon be announcing alternative plans for spending the money. The Norwegians were the most forgiving, saying they were satisfied by Uganda’s repayment of the lost money and prosecution of the guilty parties, and that they would resume funding the government.

The sweeping cuts to development aid raise the threat of painful cutbacks in Uganda’s health sector. I asked Karen Klimowski, the director of USAID Uganda’s health, HIV, and education programs, if she was worried that other donors’ shifting to USAID’s NGO-based model would put basic services in danger. Klimowski said that the withdrawn money would be redirected to NGOs and ultimately benefit the same people. She said that although as much as 80 percent of health spending in Uganda comes from foreign contributors, closer coordination between donors, NGOs, and the Ugandan government could ensure that any gaps were filled. Ultimately, she said, it was the responsibility of the Ugandan government to increase its own health spending to make up the difference.

But I was still having trouble with the math. How could the Ugandan government scale up its official health budget if direct support from donors was being cut back? I pressed Klimowski about whether the US model was sustainable.

Eventually, she described a role for NGOs that is far more long-term than the United States has officially acknowledged.

“We’ve now become realistic,” Klimowski said. “Maybe in the olden days we would have said, yes, everything needs to transfer to the government. Realistically, that’s not going to happen in these developing countries, right? You have so much need across all of their areas, right? So it’s become more realistic in what can transition and what can’t transition. What do we as donors say? This is our long term investment, and this is what we support.”

In the government’s Malaria Control Programme, Lugemwa appears to accept that there will be a greater role for NGOs. Working together to coordinate services and find arrangements that everyone can agree on is “the way forward” from Uganda’s foreign aid impasse, he said.

Despite the withdrawal of aid, Lugemwa is optimistic that Uganda’s progress on malaria and child mortality can continue. He lays out an ambitious agenda for beating back malaria with the same evangelical zeal that he defends his reputation. He returned to the government that falsely accused him, he said, to demonstrate his innocence and because his country needed his expertise.

“I quote my words when I was acquitted,” Lugemwa said. “I pity my country because it cannot tell its friend from its enemy.”

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